SMTL ID : 8z7e.1

Structure of G9a in complex with compound 9b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.64, C.77, C.107, C.111 Ligands: ZN.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.77, A:C.107, A:C.111 ZN.2: 6 residues within 4Å: Chain A: C.70, C.107, C.113, C.117 Ligands: ZN.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.70, A:C.107, A:C.113, A:C.117 ZN.3: 6 residues within 4Å: Chain A: C.64, C.66, C.70, C.75 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:C.66, A:C.70, A:C.75 ZN.4: 4 residues within 4Å: Chain A: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.258, A:C.260, A:C.265 ZN.7: 6 residues within 4Å: Chain B: C.64, C.77, C.107, C.111 Ligands: ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.77, B:C.107, B:C.111 ZN.8: 6 residues within 4Å: Chain B: C.70, C.107, C.113, C.117 Ligands: ZN.7, ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.70, B:C.107, B:C.113, B:C.117 ZN.9: 6 residues within 4Å: Chain B: C.64, C.66, C.70, C.75 Ligands: ZN.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:C.66, B:C.70, B:C.75 ZN.10: 4 residues within 4Å: Chain B: C.205, C.258, C.260, C.265 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.205, B:C.258, B:C.260, B:C.265

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.5: 17 residues within 4Å: Chain A: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, W.249, F.256, T.257, C.258, Q.259 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.244 Hydrogen bonds: A:W.140, A:S.174, A:Y.175, A:Y.175, A:R.199, A:N.202, A:N.202, A:H.203, A:H.203, A:Q.259 Water bridges: A:I.201 SFG.11: 17 residues within 4Å: Chain B: M.138, G.139, W.140, S.174, Y.175, R.199, F.200, I.201, N.202, H.203, Y.244, F.248, W.249, F.256, T.257, C.258, Q.259 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.244 Hydrogen bonds: B:W.140, B:S.174, B:Y.175, B:R.199, B:N.202, B:N.202, B:H.203, B:H.203, B:Y.244, B:Q.259 Water bridges: B:R.134, B:S.174, B:I.201

2 x 01: ~{N}-[(2~{S})-1-[[4-[(dimethylamino)methyl]phenyl]methylamino]-1-oxidanylidene-hexan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide

01.6: 18 residues within 4Å: Chain A: Y.157, D.164, A.167, D.168, D.173, S.174, L.176, F.177, D.178, N.181, C.188, P.211, R.213, F.242, D.243, Y.244, R.247, F.248 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:D.173, A:L.176, A:L.176, A:F.177, A:F.177, A:F.177, A:F.242, A:Y.244, A:Y.244, A:F.248 Hydrogen bonds: A:L.176, A:D.178, A:Y.244, A:R.247 Water bridges: A:D.164, A:N.181, A:R.247, A:F.248 Salt bridges: A:D.164, A:D.168, A:D.178 pi-Stacking: A:F.177 01.12: 17 residues within 4Å: Chain B: Y.157, D.164, A.167, S.174, L.176, F.177, D.178, D.180, C.188, P.211, R.213, F.242, D.243, Y.244, R.247, F.248, I.251 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.176, B:F.177, B:F.177, B:D.178, B:R.213, B:F.242, B:Y.244, B:Y.244, B:Y.244, B:F.248, B:I.251 Hydrogen bonds: B:L.176, B:D.178, B:Y.244, B:R.247 Water bridges: B:F.248 Salt bridges: B:D.164, B:D.168, B:D.178 pi-Stacking: B:F.177 pi-Cation interactions: B:R.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishigaya, Y. et al., Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment. Bioorg.Med.Chem.Lett. (2024)

Release Date

2025-01-22

Peptides

Histone-lysine N-methyltransferase EHMT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone-lysine N-methyltransferase EHMT2

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